A critical comparison of protein microarray fabrication technologies

Body fluid multiomics in 3PM-guided ischemic stroke management: health risk assessment, targeted protection against health-to-disease transition, and cost-effective personalized approach are envisaged

Because of its rapid progression and frequently poor prognosis, stroke is the third major cause of death in Europe and the first one in China. Many independent studies demonstrated sufficient space for prevention interventions in the primary care of ischemic stroke defined as the most cost-effective protection of vulnerable subpopulations against health-to-disease transition. Although several studies identified molecular patterns specific for IS in body fluids, none of these approaches has yet been incorporated into IS treatment guidelines. The advantages and disadvantages of individual body fluids are thoroughly analyzed throughout the paper. For example, multiomics based on a minimally invasive approach utilizing blood and its components is recommended for real-time monitoring, due to the particularly high level of dynamics of the blood as a body system. On the other hand, tear fluid as a more stable system is recommended for a non-invasive and patient-friendly holistic approach appropriate for health risk assessment and innovative screening programs in cost-effective IS management. This article details aspects essential to promote the practical implementation of highlighted achievements in 3PM-guided IS management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-024-00376-2.

Optoelectronic Tweezers Micro-Well System for Highly Efficient Single-Cell Trapping, Dynamic Sorting, and Retrieval

Single-cell arrays have emerged as a versatile method for executing single-cell manipulations across an array of biological applications. In this paper, an innovative microfluidic platform is unveiled that utilizes optoelectronic tweezers (OETs) to array and sort individual cells at a flow rate of 20 µL min-1. This platform is also adept at executing dielectrophoresis (DEP)-based, light-guided single-cell retrievals from designated micro-wells. This presents a compelling non-contact method for the rapid and straightforward sorting of cells that are hard to distinguish. Within this system, cells are individually confined to micro-wells, achieving an impressive high single-cell capture rate exceeding 91.9%. The roles of illuminating patterns, flow velocities, and applied electrical voltages are delved into in enhancing the single-cell capture rate. By integrating the OET system with the micro-well arrays, the device showcases adaptability and a plethora of functions. It can concurrently trap and segregate specific cells, guided by their dielectric signatures. Experimental results, derived from a mixed sample of HepG2 and L-O2 cells, reveal a sorting accuracy for L-O2 cells surpassing 91%. Fluorescence markers allow for the identification of sequestered, fluorescence-tagged HepG2 cells, which can subsequently be selectively released within the chip. This platform's rapidity in capturing and releasing individual cells augments its potential for future biological research and applications.

Endophytic fungi as a potential source of anti-cancer drug

Endophytes are considered one of the major sources of bioactive compounds used in different aspects of health care including cancer treatment. When colonized, they either synthesize these bioactive compounds as a part of their secondary metabolite production or augment the host plant machinery in synthesising such bioactive compounds. Hence, the study of endophytes has drawn the attention of the scientific community in the last few decades. Among the endophytes, endophytic fungi constitute a major portion of endophytic microbiota. This review deals with a plethora of anti-cancer compounds derived from endophytic fungi, highlighting alkaloids, lignans, terpenes, polyketides, polyphenols, quinones, xanthenes, tetralones, peptides, and spirobisnaphthalenes. Further, this review emphasizes modern methodologies, particularly omics-based techniques, asymmetric dihydroxylation, and biotic elicitors, showcasing the dynamic and evolving landscape of research in this field and describing the potential of endophytic fungi as a source of anticancer drugs in the future.

Unlocking Bio-Instructive Polymers: A Novel Multi-Well Screening Platform Based on Secretome Sampling

Biomaterials are designed to interact with biological systems to replace, support, enhance, or monitor their function. However, there are challenges associated with traditional biomaterials' development due to the lack of underlying theory governing cell response to materials' chemistry. This leads to the time-consuming process of testing different materials plus the adverse reactions in the body such as cytotoxicity and foreign body response. High-throughput screening (HTS) offers a solution to these challenges by enabling rapid and simultaneous testing of a large number of materials to determine their bio-interactions and biocompatibility. Secreted proteins regulate many physiological functions and determine the success of implanted biomaterials through directing cell behaviour. However, the majority of biomaterials' HTS platforms are suitable for microscopic analyses of cell behaviour and not for investigating non-adherent cells or measuring cell secretions. Here, we describe a multi-well platform adaptable to robotic printing of polymers and suitable for secretome profiling of both adherent and non-adherent cells. We detail the platform's development steps, encompassing the preparation of individual cell culture chambers, polymer printing, and the culture environment, as well as examples to demonstrate surface chemical characterisation and biological assessments of secreted mediators. Such platforms will no doubt facilitate the discovery of novel biomaterials and broaden their scope by adapting wider arrays of cell types and incorporating assessments of both secretome and cell-bound interactions. Key features • Detailed protocols for preparation of substrate for contact printing of acrylate-based polymers including O2 plasma etching, functionalisation process, and Poly(2-hydroxyethyl methacrylate) (pHEMA) dip coating. • Preparations of 7 mm × 7 mm polymers employing pin printing system. • Provision of confined area for each polymer using ProPlate® multi-well chambers. • Compatibility of this platform was validated using adherent cells [primary human monocyte-derived macrophages (MDMs)) and non-adherent cells (primary human monocyte-derived dendritic cells (moDCs)]. • Examples of the adaptability of the platform for secretome analysis including five different cytokines using enzyme-linked immunosorbent assay (ELISA, DuoSet®). Graphical overview.

Proteome microarray identifies autoantibody biomarkers for diagnosis of hepatitis B-related hepatocellular carcinoma

BACKGROUND AND AIMS

Hepatocellular carcinoma (HCC) has the highest mortality rate among malignant tumors worldwide. This study aimed to analyze the biological characteristics of serum proteins in hepatitis B (HBV)-related liver diseases, identify diagnostic biomarkers for HBV-infected HCC, and provide a scientific basis for its prevention and treatment.

MATERIALS AND METHODS

We used HuProt arrays to identify candidate biomarkers for HBV-related liver diseases and verified the differential biomarkers by using an HCC-focused array. The biological characteristics of serum proteins were analyzed via bioinformatics. Serum biomarkers levels were validated by ELISA.

RESULTS

We identified 547 differentially expressed proteins from HBV-infected HCC in a screening cohort. After analyzing the biological characteristics of serum proteins, we identified 10 potential differential autoantibodies against tumor-associated antigens (TAAbs) and a candidate biomarker panel (APEX2, RCSD1, and TP53) for the diagnosis of HBV-associated HCC with 61.9% sensitivity and 81.7% specificity in an HCC-focused array validation cohort. Finally, the protein levels and diagnostic capability of the biomarker panel were confirmed in a large-sample validation cohort, and this panel was found to be superior to alpha-fetoprotein, the standard hallmark for the diagnosis of HCC.

CONCLUSION

The APEX2, RCSD1, and TP53 biomarker panels could be used for the diagnosis of HBV-associated HCC, providing a scientific basis for clinical practice.

Data-driven decision-making for precision diagnosis of digestive diseases

Modern omics technologies can generate massive amounts of biomedical data, providing unprecedented opportunities for individualized precision medicine. However, traditional statistical methods cannot effectively process and utilize such big data. To meet this new challenge, machine learning algorithms have been developed and applied rapidly in recent years, which are capable of reducing dimensionality, extracting features, organizing data and forming automatable data-driven clinical decision systems. Data-driven clinical decision-making have promising applications in precision medicine and has been studied in digestive diseases, including early diagnosis and screening, molecular typing, staging and stratification of digestive malignancies, as well as precise diagnosis of Crohn's disease, auxiliary diagnosis of imaging and endoscopy, differential diagnosis of cystic lesions, etiology discrimination of acute abdominal pain, stratification of upper gastrointestinal bleeding (UGIB), and real-time diagnosis of esophageal motility function, showing good application prospects. Herein, we reviewed the recent progress of data-driven clinical decision making in precision diagnosis of digestive diseases and discussed the limitations of data-driven decision making after a brief introduction of methods for data-driven decision making.

Protein array processing software for automated semiquantitative analysis of serum antibody repertoires

Effective immunotherapies activate natural antitumor immune responses in patients undergoing treatment. The ability to monitor immune activation in response to immunotherapy is critical in measuring treatment efficacy over time and across patient cohorts. Protein arrays are systematically arranged, large collections of annotated proteins on planar surfaces, which can be used for the characterization of disease-specific and treatment-induced antibody repertoires in individuals undergoing immunotherapy. However, the absence of appropriate image analysis and data processing software presents a substantial hurdle, limiting the uptake of this approach in immunotherapy research. We developed a first, automated semiquantitative open-source software package for the analysis of widely used protein macroarrays. The software allows accurate single array and inter-array comparative studies through the tackling of intra-array inconsistencies arising from experimental disparities. The innovative and automated image analysis process includes adaptive positioning, background identification and subtraction, removal of null signals, robust statistical analysis, and protein pair validation. The normalized values allow a convenient semiquantitative data analysis of different samples or timepoints. Enabling accurate characterization of sample series to identify disease-specific immune profiles or their relative changes in response to treatment may serve as a diagnostic or predictive tool of disease.

Synthetic Approaches of Epoxysuccinate Chemical Probes

Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.

A protein microarray-based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer

PURPOSE

Colorectal cancer (CRC) has been reported as the second leading cause of cancer death worldwide. The 5-year annual survival is around 50%, mainly due to late diagnosis, striking necessity for early detection. This study aims to identify autoantibody in patients' sera for early screening of cancer.

EXPERIMENTAL DESIGN

The study used a high-density human proteome array with approximately 17,000 recombinant proteins. Screening of sera from healthy individuals, CRC from Indian origin, and CRC from middle-east Asia origin were performed. Bio-statistical analysis was performed to identify significant autoantibodies altered. Pathway analysis was performed to explore the underlying mechanism of the disease.

RESULTS

The comprehensive proteomic analysis revealed dysregulation of 15 panels of proteins including CORO7, KCNAB1, WRAP53, NDUFS6, KRT30, and COLGALT2. Further biological pathway analysis for the top dysregulated autoantigenic proteins revealed perturbation in important biological pathways such as ECM degradation and cytoskeletal remodeling etc. CONCLUSIONS AND CLINICAL RELEVANCE: The generation of an autoimmune response against cancer-linked pathways could be linked to the screening of the disease. The process of immune surveillance can be detected at an early stage of cancer. Moreover, AAbs can be easily extracted from blood serum through the least invasive test for disease screening.

Comparison of blocking reagents for antibody microarray-based immunoassays on glass and paper membrane substrates

Background noise due to nonspecific binding of biomolecules on the assay substrates is one of the most common challenges that limits the sensitivity of microarray-based immunoassays. Background signal intensity usually increases when complex biological fluids are used because they have a combination of molecules and vesicles that can adsorb onto substrate surfaces. Blocking strategies coupled with surface chemistries can reduce such nonspecific binding and improve assay sensitivity. In this paper, we conducted a systematic optimization of blocking strategies on a variety of commonly used substrates for protein measurement in complex biofluids. Four blocking strategies (BSA, non-fat milk, PEG, and a protein-free solution) coupled with four surface chemistries (3-glycidoxypropyltrimethoxysilane (GPS), poly-L-lysine (PLL), aminoalkylsilane (AAS), and nitrocellulose (NC)) were studied for their effect on background, microspot, and net signal intensities. We have also explored the effect that these blocking strategies have when proteins in complex samples (plasma, serum, cell culture media, and EV lysate) are measured. Irregular spot morphology could affect signal extraction using automated software. We found that the microspots with the best morphology were the ones printed on GPS glass surfaces for all immunoassays. On NC membrane, the protein-based blocking strategies yielded the highest net fluorescent intensity with the antigen contained in PBS, plasma, serum, and serum-free cell culture media. Differently, with EV lysate samples, Pierce™ protein-free blocker yielded the best net signal intensity on both GPS and NC surfaces. The choice of blocking strategies highly depends on the substrate. Moreover, the findings discovered in this study are not limited to microarray-based immunoassays but can provide insights for other assay formats.

Research progress in protein microarrays: Focussing on cancer research

Although several effective treatment modalities have been developed for cancers, the morbidity and mortality associated with cancer continues to increase every year. As one of the most exciting emerging technologies, protein microarrays represent a powerful tool in the field of cancer research because of their advantages such as high throughput, small sample usage, more flexibility, high sensitivity and direct readout of results. In this review, we focus on the research progress in four types of protein microarrays (proteome microarray, antibody microarray, lectin microarray and reversed protein array) with emphasis on their application in cancer research. Finally, we discuss the current challenges faced by protein microarrays and directions for future developments. We firmly believe that this novel systems biology research tool holds immense potential in cancer research and will become an irreplaceable tool in this field.

Biofunctionalization of Multiplexed Silicon Photonic Biosensors

Silicon photonic (SiP) sensors offer a promising platform for robust and low-cost decentralized diagnostics due to their high scalability, low limit of detection, and ability to integrate multiple sensors for multiplexed analyte detection. Their CMOS-compatible fabrication enables chip-scale miniaturization, high scalability, and low-cost mass production. Sensitive, specific detection with silicon photonic sensors is afforded through biofunctionalization of the sensor surface; consequently, this functionalization chemistry is inextricably linked to sensor performance. In this review, we first highlight the biofunctionalization needs for SiP biosensors, including sensitivity, specificity, cost, shelf-stability, and replicability and establish a set of performance criteria. We then benchmark biofunctionalization strategies for SiP biosensors against these criteria, organizing the review around three key aspects: bioreceptor selection, immobilization strategies, and patterning techniques. First, we evaluate bioreceptors, including antibodies, aptamers, nucleic acid probes, molecularly imprinted polymers, peptides, glycans, and lectins. We then compare adsorption, bioaffinity, and covalent chemistries for immobilizing bioreceptors on SiP surfaces. Finally, we compare biopatterning techniques for spatially controlling and multiplexing the biofunctionalization of SiP sensors, including microcontact printing, pin- and pipette-based spotting, microfluidic patterning in channels, inkjet printing, and microfluidic probes.

Integrated silicon microfluidic chip for picoliter-scale analyte segmentation and microscale printing for mass spectrometry imaging

A silicon single-chip microfluidics system that integrates microscale fluidic channels, an analyte segmentation device, and a nozzle for electrohydrodynamic-assisted printing is designed for hyphenation with MALDI mass spectrometry (MS) imaging. A miniaturized T-junction segments analytes into monodisperse picoliter oil-isolated compartments. The printing nozzle deposits generated droplets one-by-one into an array on a conductive substrate without splitting or coalescing. Virtually single-shot MS analysis is enabled due to the ultrasmall droplet volumes and highly localized printing. The signal-to-noise ratio indicates that detection limits at the attomole level are achieved for γ-aminobutyric acid.

Optimization of an Antibody Microarray Printing Process Using a Designed Experiment

Antibody microarrays have proven useful in immunoassay-based point-of-care diagnostics for infectious diseases. Noncontact piezoelectric inkjet printing has advantages to print antibody microarrays on nitrocellulose substrates for this application due to its compatibility with sensitive solutions and substrates, simple droplet control, and potential for high-capacity printing. However, there remain real-world challenges in printing such microarrays, which motivated this study. The effects of three concentrations of capture antibody (cAb) reagents and nozzle hydrostatic pressures were chosen to investigate three responses: the number of printed membrane disks, dispensing performance, and microarray quality. Printing conditions were found to be most ideal with 5 mg/mL cAb and a nozzle hydrostatic pressure near zero, which produced 130 membrane disks in a single print versus the 10 membrane disks per print before optimization. These results serve to inform efficient printing of antibody microarrays on nitrocellulose membranes for rapid immunoassay-based detection of infectious diseases and beyond.

Meta-Analysis of Human Antibodies Against Plasmodium falciparum Variable Surface and Merozoite Stage Antigens

Concerted efforts to fight malaria have caused significant reductions in global malaria cases and mortality. Sustaining this will be critical to avoid rebound and outbreaks of seasonal malaria. Identifying predictive attributes that define clinical malaria will be key to guide development of second-generation tools to fight malaria. Broadly reactive antibodies against variable surface antigens that are expressed on the surface of infected erythrocytes and merozoites stage antigens are targets of naturally acquired immunity and prime candidates for anti-malaria therapeutics and vaccines. However, predicting the relationship between the antigen-specific antibodies and protection from clinical malaria remains unresolved. Here, we used new datasets and multiple approaches combined with re-analysis of our previous data to assess the multi-dimensional and complex relationship between antibody responses and clinical malaria outcomes. We observed 22 antigens (17 PfEMP1 domains, 3 RIFIN family members, merozoite surface protein 3 (PF3D7_1035400), and merozoites-associated armadillo repeats protein (PF3D7_1035900) that were selected across three different clinical malaria definitions (1,000/2,500/5,000 parasites/µl plus fever). In addition, Principal Components Analysis (PCA) indicated that the first three components (Dim1, Dim2 and Dim3 with eigenvalues of 306, 48, and 29, respectively) accounted for 66.1% of the total variations seen. Specifically, the Dim1, Dim2 and Dim3 explained 52.8%, 8.2% and 5% of variability, respectively. We further observed a significant relationship between the first component scores and age with antibodies to PfEMP1 domains being the key contributing variables. This is consistent with a recent proposal suggesting that there is an ordered acquisition of antibodies targeting PfEMP1 proteins. Thus, although limited, and further work on the significance of the selected antigens will be required, these approaches may provide insights for identification of drivers of naturally acquired protective immunity as well as guide development of additional tools for malaria elimination and eradication.

Technologies for Frugal and Sensitive Point-of-Care Immunoassays

Immunoassays are a powerful tool for sensitive and quantitative analysis of a wide range of biomolecular analytes in the clinic and in research laboratories. However, enzyme-linked immunosorbent assay (ELISA)-the gold-standard assay-requires significant user intervention, time, and clinical resources, making its deployment at the point-of-care (POC) impractical. Researchers have made great strides toward democratizing access to clinical quality immunoassays at the POC and at an affordable price. In this review, we first summarize the commercially available options that offer high performance, albeit at high cost. Next, we describe strategies for the development of frugal POC assays that repurpose consumer electronics and smartphones for the quantitative detection of analytes. Finally, we discuss innovative assay formats that enable highly sensitive analysis in the field with simple instrumentation.

Lithographic Processes for the Scalable Fabrication of Micro- and Nanostructures for Biochips and Biosensors

Since the early 2000s, extensive research has been performed to address numerous challenges in biochip and biosensor fabrication in order to use them for various biomedical applications. These biochips and biosensor devices either integrate biological elements (e.g., DNA, proteins or cells) in the fabrication processes or experience post fabrication of biofunctionalization for different downstream applications, including sensing, diagnostics, drug screening, and therapy. Scalable lithographic techniques that are well established in the semiconductor industry are now being harnessed for large-scale production of such devices, with additional development to meet the demand of precise deposition of various biological elements on device substrates with retained biological activities and precisely specified topography. In this review, the lithographic methods that are capable of large-scale and mass fabrication of biochips and biosensors will be discussed. In particular, those allowing patterning of large areas from 10 cm² to m², maintaining cost effectiveness, high throughput (>100 cm² h^-1), high resolution (from micrometer down to nanometer scale), accuracy, and reproducibility. This review will compare various fabrication technologies and comment on their resolution limit and throughput, and how they can be related to the device performance, including sensitivity, detection limit, reproducibility, and robustness.

Light Absorption Measurement With a CMOS Biochip for Quantitative Immunoassay Based Point-of-Care Applications

We present a CMOS biochip-based photometer for quantitative immunoassay diagnostics. The photometer quantifies the concentration of antigens based on light absorption, which allows for a low-cost implementation without expensive optical components. We propose a light controller to lower the start-up and settling time of the light source to 30 seconds, to facilitate fast measurement starts, and to decrease the overall measurement times. The application-specific integrated circuit (ASIC) contains a 6 x 7-sensor array with 100 μm x 100 μm photodiodes that serve as signal transducers. The ASIC was developed in a normal 0.35- μm CMOS technology, avoiding the need for expensive post-CMOS processes. We present our strategy for the assembly of the ASIC and the immobilization of antibodies. For its first time, we demonstrate the quantification of prostate specific antigen (PSA) with an optoelectronic CMOS biochip using this approach. A PSA immunoassay is performed on the top surface of the CMOS sensor array, enzyme kinetics and PSA concentration are measured within 6 minutes with a limit of detection (LoD) of 0.5 ng/ml, which meets clinical testing requirements. We achieve an overall coefficient of variation (CV) of 7%, which is good compared to other point-of-care (PoC) systems.

High sensitivity analysis of nanogram quantities of glycosaminoglycans using ToF-SIMS

Glycosaminoglycans (GAGs) are important biopolymers that differ in the sequence of saccharide units and in post polymerisation alterations at various positions, making these complex molecules challenging to analyse. Here we describe an approach that enables small quantities (<200 ng) of over 400 different GAGs to be analysed within a short time frame (3-4 h). Time of flight secondary ion mass spectrometry (ToF-SIMS) together with multivariate analysis is used to analyse the entire set of GAG samples. Resultant spectra are derived from the whole molecules and do not require pre-digestion. All 6 possible GAG types are successfully discriminated, both alone and in the presence of fibronectin. We also distinguish between pharmaceutical grade heparin, derived from different animal species and from different suppliers, to a sensitivity as low as 0.001 wt%. This approach is likely to be highly beneficial in the quality control of GAGs produced for therapeutic applications and for characterising GAGs within biomaterials or from in vitro cell culture.

Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology

Cell-free protein synthesis (CFPS) systems are gaining more importance as universal tools for basic research, applied sciences, and product development with new technologies emerging for their application. Huge progress was made in the field of synthetic biology using CFPS to develop new proteins for technical applications and therapy. Out of the available CFPS systems, wheat germ cell-free protein synthesis (WG-CFPS) merges the highest yields with the use of a eukaryotic ribosome, making it an excellent approach for the synthesis of complex eukaryotic proteins including, for example, protein complexes and membrane proteins. Separating the translation reaction from other cellular processes, CFPS offers a flexible means to adapt translation reactions to protein needs. There is a large demand for such potent, easy-to-use, rapid protein expression systems, which are optimally serving protein requirements to drive biochemical and structural biology research. We summarize here a general workflow for a wheat germ system providing examples from the literature, as well as applications used for our own studies in structural biology. With this review, we want to highlight the tremendous potential of the rapidly evolving and highly versatile CFPS systems, making them more widely used as common tools to recombinantly prepare particularly challenging recombinant eukaryotic proteins.

Bioprinting 3D human cardiac tissue chips using the pin type printer 'microscopic painting device' and analysis for cardiotoxicity

In this study, three-dimensional (3D) cardiac tissue constructed using the pin type bioprinter 'microscopic painting device' and layer-by-layer cell coating technique was confirmed to have drug responsiveness by three different analytical methods for cardiotoxicity assay. Recently, increasing attention has been focused on biofabrication to create biomimetic 3D tissue. Although various tissues can be produced in vitro, there are many issues surrounding the stability and reproducibility of the preparation of 3D tissues. Thus, although many bioprinters have been developed, none can efficiently, reproducibly and precisely produce small 3D tissues (μm-mm order) such as spheroids, which are most commonly used in drug development. The 3D cardiac tissue chips were successfully constructed with a similar number of cells as conventional 2D tissue using a pin type bioprinter, and corresponding drug-induced cardiotoxicities were obtained with known compounds that induce cardiotoxicity. The 3D cardiac tissue chips displayed uniform cell density and completely synchronized electrophysiological properties as compared to 2D tissue. The 3D tissues constructed using a pin type bioprinter as a biofabrication device would be promising tools for cardiotoxicity assay as they are capable of obtaining stable and reproducible data, which cannot be obtained by 2D tissue.

Composable Microfluidic Plates (cPlate): A Simple and Scalable Fluid Manipulation System for Multiplexed Enzyme-Linked Immunosorbent Assay (ELISA)

Enzyme-linked immunosorbent assay (ELISA) is the gold standard method for protein biomarkers. However, scaling up ELISA for multiplexed biomarker analysis is not a trivial task due to the lengthy procedures for fluid manipulation and high reagent/sample consumption. Herein, we present a highly scalable multiplexed ELISA that achieves a similar level of performance to commercial single-target ELISA kits as well as shorter assay time, less consumption, and simpler procedures. This ELISA is enabled by a novel microscale fluid manipulation method, composable microfluidic plates (cPlate), which are comprised of miniaturized 96-well plates and their corresponding channel plates. By assembling and disassembling the plates, all of the fluid manipulations for 96 independent ELISA reactions can be achieved simultaneously without any external fluid manipulation equipment. Simultaneous quantification of four protein biomarkers in serum samples is demonstrated with the cPlate system, achieving high sensitivity and specificity (∼ pg/mL), short assay time (∼1 h), low consumption (∼5 μL/well), high scalability, and ease of use. This platform is further applied to probe the levels of three protein biomarkers related to vascular dysfunction under pulmonary nanoparticle exposure in rat's plasma. Because of the low cost, portability, and instrument-free nature of the cPlate system, it will have great potential for multiplexed point-of-care testing in resource-limited regions.

Protein patterning with antifouling polymer gel platforms generated using visible light irradiation

Visible light-assisted protein patterning on a solid surface was performed with phosphorylcholine (PC) polymers bearing tyrosine residues. Because of the antifouling nature of PC polymers, protein immobilisation was regiospecifically controlled, thus enabling the microfabricated surfaces to be used as immunoassay platforms.

Reverse Phase Protein Arrays

Reverse phase protein arrays (RPPA) are used to quantify proteins and protein posttranslational modifications in cellular lysates and body fluids. RPPA technology is suitable for biomarker discovery, protein pathway profiling, functional phenotype analysis, and drug discovery mechanism of action. The principles of RPPA technology are (a) immobilizing protein-containing specimens on a coated slide in discrete spots, (b) antibody recognition of proteins, (c) amplification chemistries to detect the protein-antibody complex, and (d) quantifying spot intensity. Construction of a RPPA begins with the robotic liquid transfer of protein-containing specimens from microtiter plates onto nitrocellulose-coated slides. The robotic arrayer deposits each sample as discrete spots in an array format. Specimens, controls, and calibrators are printed on each array, thus providing a complete calibrated assay on a single slide. Each RPPA slide is subsequently probed with catalyzed signal amplification chemistries and a single primary antibody, a secondary antibody, and either fluorescent or colorimetric dyes. The focus of this chapter is to describe RPPA detection and imaging using a colorimetric (diaminobenzidine (DAB)) detection strategy.

Reagent integration and controlled release for multiplexed nucleic acid testing in disposable thermoplastic 2D microwell arrays

The seamless integration of reagents into microfluidic devices can serve to significantly reduce assay complexity and cost for disposable diagnostics. In this work, the integration of multiplexed reagents into thermoplastic 2D microwell arrays is demonstrated using a scalable pin spotting technique. Using a simple and low-cost narrow-bore capillary spotting pin, high resolution deposition of concentrated reagents within the arrays of enclosed nanoliter-scale wells is achieved. The pin spotting method is further employed to encapsulate the deposited reagents with a chemically modified wax layer that serves to prevent disruption of the dried assay components during sample introduction through a shared microchannel, while also enabling temperature-controlled release after sample filling is complete. This approach supports the arbitrary patterning and release of different reagents within individual wells without crosstalk for multiplexed analyses. The performance of the in-well spotting technique is characterized using on-chip rolling circle amplification to evaluate its potential for nucleic acid-based diagnostics.

Antibody Printing Technologies

Antibody microarrays are routinely employed in the lab and in the clinic for studying protein expression, protein-protein, and protein-drug interactions. The microarray format reduces the size scale at which biological and biochemical interactions occur, leading to large reductions in reagent consumption and handling times while increasing overall experimental throughput. Specifically, antibody microarrays, as a platform, offer a number of different advantages over traditional techniques in the areas of drug discovery and diagnostics. While a number of different techniques and approaches have been developed for creating micro and nanoscale antibody arrays, issues relating to sensitivity, cost, and reproducibility persist. The aim of this review is to highlight current state-of the-art techniques and approaches for creating antibody arrays by providing latest accounts of the field while discussing potential future directions.

Immunoassay Biosensing of Foodborne Pathogens with Surface Plasmon Resonance Imaging: A Review

Surface plasmon resonance imaging (SPRi) has been increasingly used in the label-free detections of various biospecies, such as organic toxins, proteins, and bacteria. In combination with the well-developed microarray immunoassay, SPRi has the advantages of rapid detection in tens of minutes and multiplex detection of different targets with the same biochip. Both prism-based and prism-free configurations of SPRi have been developed for highly integrated portable immunosensors, which have shown great potential on pathogen detection and living cell imaging. This review summarizes the recent advances in immunoassay biosensing with SPRi, with special emphasis on the multiplex detections of foodborne pathogens. Additionally, various spotting techniques, surface modification protocols, and signal amplification methods have been developed to improve the specificity and sensitivity of the SPRi biochip. The challenges in multiplex detections of foodborne pathogens in real-world samples are addressed, and future perspectives of miniaturizing SPRi immunosensors with nanotechnologies are discussed.

Microprocessing on Single Protein Crystals Using Femtosecond Pulse Laser

Proteins with different micropatterns have various applications in biosensing, structural analysis, and other biomedical fields. However, processing of micropatterns on single protein crystals remains a challenge due to the fragility of protein molecules. In this work, we studied femtosecond laser processing on single hen egg white lysozyme protein crystals. Optimized laser parameters were found to achieve micropatterning without cracking of protein crystals. The ablation morphology dependence on the laser fluence and the pulse number was discussed to control the processing results. Under a laser fluence higher than 1 J/cm², the ablation hole was formed. While multipulses with fluence lower than the ablation threshold were applied, the foaming area was observed due to the denaturation of protein. The numerical simulation shows that the ablation results were influenced by the ionization and energy deposition process. Micropatterns including lines, areas, and microarrays can be processed with a minimum size of 2 μm. Processed patterns on the crystal surface can be used for biosensing microarrays and the enhancement of crystal growth. The microprocessing method proposed in this study has potential applications in different fields including biodevices and biomedicine.

Art-on-a-Chip: Preserving Microfluidic Chips for Visualization and Permanent Display

"After a certain high level of technical skill is achieved, science and art tend to coalesce in aesthetics, plasticity, and form. The greatest scientists are always artists as well." said Albert Einstein. Currently, photographic images bridge the gap between microfluidic/lab-on-a-chip devices and art. However, the microfluidic chip itself should be a form of art. Here, novel vibrant epoxy dyes are presented in combination with a simple process to fill and preserve microfluidic chips, to produce microfluidic art or art-on-a-chip. In addition, this process can be used to produce epoxy dye patterned substrates that preserve the geometry of the microfluidic channels-height within 10% of the mold master. This simple approach for preserving microfluidic chips with vibrant, colorful, and long-lasting epoxy dyes creates microfluidic chips that can easily be visualized and photographed repeatedly, for at least 11 years, and hence enabling researchers to showcase their microfluidic chips to potential graduate students, investors, and collaborators.

Acoustic Patterning of Growth Factor for Three-Dimensional Tissue Engineering

Temporal and spatial presentations of biological cues are critical for tissue engineering. There is a great need in improving the incorporation of bioagent(s) (specifically growth factor(s) [GF(s)]) onto three-dimensional scaffolds. In this study, we developed a process to combine additive manufacturing (AM) technology with acoustic droplet ejection (ADE) technology to control GF distribution. More specifically, we implemented ADE to control the distribution of recombinant human bone morphogenetic protein-2 (rhBMP-2) onto polycaprolactone (PCL)-based tissue engineering constructs (TECs). Three substrates were used in this study: (1) succinimide-terminated PCL (PCL-N-hydroxysuccinimide [NHS]) as model material, (2) alkali-treated PCL (PCL-NaOH) as first control material, and (3) fibrin-coated PCL (PCL-Fibrin) as second control material. It was shown that our process enables a pattern of BMP-2 spots of ∼250 μm in diameter with ∼700 μm center-to-center spacing. An initial concentration of BMP-2 higher than 300 μg/L was required to retain a detectable amount of GF on the substrate after a wash with phosphate-buffered solution. However, to obtain detectable osteogenic differentiation of C2C12 cells, the initial concentration of BMP-2 higher than 750 μg/L was needed. The cells on PCL-NHS samples showed spatial alkaline phosphatase staining correlating with local patterns of BMP-2, although the intensity was lower than the controls (PCL-NaOH and PCL-Fibrin). Our results have demonstrated that the developed AM-ADE process holds great promise in creating TECs with highly controlled GF patterning. Impact statement The combined process of additive manufacturing with acoustic droplet ejection to control growth factor (GF) distribution across three-dimensional (3D) porous scaffolds that is presented in this study enables creating 3D tissue engineering constructs with highly controlled GF patterning. Such constructs enable temporal and spatial presentations of biological cues for enhancing cell migration and differentiation and eventually the formation of targeted tissues in vitro and in vivo.

Multivalent glycan arrays

Glycan microarrays have become a powerful technology to study biological processes, such as cell-cell interaction, inflammation, and infections. Yet, several challenges, especially in multivalent display, remain. In this introductory lecture we discuss the state-of-the-art glycan microarray technology, with emphasis on novel approaches to access collections of pure glycans and their immobilization on surfaces. Future directions to mimic the natural glycan presentation on an array format, as well as in situ generation of combinatorial glycan collections, are discussed.

Technological Advances in Preclinical Drug Evaluation: The Role of -Omics Methods

Preclinical drug development is an essential step in the drug development process where the evaluation of new chemical entities occurs. In particular, preclinical drug development phases include deep analysis of drug candidates' interactions with biomolecules/targets, their safety, toxicity, pharmacokinetics, metabolism by use of assays in vitro and in vivo animal assays. Legal aspects of the required procedures are well-established. Herein, we present a comprehensive summary of current state-of-the art approaches and techniques used in preclinical studies. In particular, we will review the potential of new, -omics methods and platforms for mechanistic evaluation of drug candidates and speed-up of the preclinical evaluation steps.

Customizable Multiplex Antibody Array Immunoassays with Attomolar Sensitivities

We have developed a customizable contact printed multiplex immunoassay capable of simultaneously measuring up to five analytes with attomolar sensitivities. This enzyme-linked immunosorbent assay (ELISA) was based on spotting different antibodies in a circular pattern at the bottom of a microtiter plate well. Unlike traditional antibody printing for ELISA that prints a capture antibody specific to a target of interest, in this ELISA we printed unique "anchor" antibodies at the well surface, each having a high affinity for a specific peptide target. By coupling each peptide to a unique assay capture antibody, this array of anchor antibodies enabled a customizable contact printed multiplex immunoassay workflow. As a proof of concept, we developed a 5-plex assay measuring interleukin 5 (IL-5), interleukin 6 (IL-6), interleukin 10 (IL-10), interleukin 22 (IL-22), and tumor necrosis factor alpha (TNF-α). Measurements of these five analytes in serum and plasma correlated well between the method utilizing the anchor antibodies and peptides and the traditional capture antibody printing approach, with r² values of 0.99, 0.93, 0.99, 0.96, and 0.75 for IL-5, IL-6, IL-10, IL-22, and TNFα, respectively. This approach makes customizable multiplex ultrasensitive ELISA available to laboratories without access to the precision printing instrumentation and will be useful for antibody screening, custom assay development, biomarker detection, and protein profiling for diagnostic applications.

Light-assisted drying for anhydrous preservation of biological samples: optical characterization of the trehalose preservation matrix

Protein-based drugs have been developed to treat a variety of conditions and assays use immobilized capture proteins for disease detection. Freeze-drying is currently the standard for the preservation of proteins, but this method is expensive and requires lengthy processing times. Anhydrous preservation in a trehalose amorphous solid matrix offers a promising alternative to freeze-drying. Light assisted drying (LAD) is a processing method to create an amorphous trehalose matrix. Proteins suspended in a trehalose solution are dehydrated using near-infrared laser light. The laser radiation accelerates drying and as water is removed the trehalose forms a protective matrix. In this work, LAD samples are characterized to determine the crystallization kinetics of the trehalose after LAD processing and the distribution of amorphous trehalose in the samples. These characteristics influence the long-term stability of the samples. Polarized light imaging revealed that LAD processed samples are stable against crystallization during low-humidity storage at room temperature. Scanning white light interferometry and Raman spectroscopy indicated that trehalose was present across samples in an amorphous form. In addition, differential scanning microcalorimetry was used to measure the thermodynamic characteristics of the protein lysozyme after LAD processing. These results demonstrate that LAD does not change the properties of this protein.

The Surface Science of Microarray Generation-A Critical Inventory

Microarrays are powerful tools in biomedical research and have become indispensable for high-throughput multiplex analysis, especially for DNA and protein analysis. The basis for all microarray processing and fabrication is surface modification of a chip substrate and many different strategies to couple probe molecules to such substrates have been developed. We present here a critical assessment of typical biochip generation processes from a surface science point of view. While great progress has been made from a molecular biology point of view on the development of qualitative assays and impressive results have been obtained on the detection of rather low concentrations of DNA or proteins, quantitative chip-based assays are still comparably rare. We argue that lack of stable and reliable deposition chemistries has led in many cases to suboptimal quantitative reproducibility, impeded further progress in microarray development and prevented a more significant penetration of microarray technology into the diagnostic market. We suggest that surface-attached hydrogel networks might be a promising strategy to achieve highly sensitive and quantitatively reproducible microarrays.

Single molecule protein patterning using hole mask colloidal lithography

The ability to manipulate single protein molecules on a surface is useful for interfacing biology with many types of devices in optics, catalysis, bioengineering, and biosensing. Control of distance, orientation, and activity at the single molecule level will allow for the production of on-chip devices with increased biological activity. Cost effective methodologies for single molecule protein patterning with tunable pattern density and scalable coverage area remain a challenge. Herein, Hole Mask Colloidal Lithography is presented as a bench-top colloidal lithography technique that enables a glass coverslip to be patterned with functional streptavidin protein onto patches from 15-200 nm in diameter with variable pitch. Atomic force microscopy (AFM) was used to characterize the size of the patterned features on the glass surface. Additionally, single-molecule fluorescence microscopy was used to demonstrate the tunable pattern density, measure binding controls, and confirm patterned single molecules of functional streptavidin.

Lamb wave-based molecular diagnosis using DNA hydrogel formation by rolling circle amplification (RCA) process

Recent developments in microfluidics enable the lab-on-a-chip-based molecular diagnosis. Rapid and accurate diagnosis of infectious diseases is critical for preventing the transmission of the disease. Here, we characterize a Lamb wave-based device using various parameters including the contact angle and viscosity of the sample droplet, the applied voltage, and the temperature increase. Additionally, we demonstrate the functionality of the Lamb wave-based device in clinical application. Optimal temperature for rolling circle amplification (RCA) process is 30 °C, and it was achieved by Lamb wave generation at 17 V. Gene amplification due to RCA process could be detected by viscosity increase due to DNA hydrogel formation in a sample droplet, which induced the acoustic streaming velocity of suspended particles to be decreased. In our Lamb wave-based device, isothermal amplification of target nucleic acids could be successfully detected within 30 min using 10 μL of sessile droplet, and was validated by comparing that of commercial real-time fluorescence analysis. Our device enables simple and low-cost molecular diagnosis, which can be applied to resource-limited clinical settings.

Advances in Surface Plasmon Resonance Imaging and Microscopy and Their Biological Applications

Surface plasmon resonance microscopy and imaging are optical methods that enable observation and quantification of interactions of nano- and microscale objects near a metal surface in a temporally and spatially resolved manner. This review describes the principles of surface plasmon resonance microscopy and imaging and discusses recent advances in these methods, in particular, in optical platforms and functional coatings. In addition, the biological applications of these methods are reviewed. These include the detection of a broad variety of analytes (nucleic acids, proteins, bacteria), the investigation of biological systems (bacteria and cells), and biomolecular interactions (drug-receptor, protein-protein, protein-DNA, protein-cell).

Meeting the challenge of developing food crops with improved nutritional quality and food safety: leveraging proteomics and related omics techniques

Eliminating malnutrition remains an imminent priority in our efforts to achieve food security and providing adequate calories, proteins, and micronutrients to the growing world population. Malnutrition may be attributed to socio-economic factors (poverty and limited accessibility to nutritional food), dietary preferences, inherent nutrient profiles of traditional food crops, and to a combination of all such factors. Modern advancements in "omics" technology have made it possible to reliably predict, diagnose, and suggest ways to remedy the low protein content and bioavailability of key micronutrients in food crops. In this review, we briefly describe how proteomics techniques can potentially be used for improving the nutrient profile of major crops, through high throughput multiplexed assays. Food safety is another important issue where proteomics and related platforms can offer solution for absolute quantitation of food allergens and mycotoxins present in the plant-based food. The purpose of the present review is to discuss the proteomic-based strategies in food crops to meet the challenges of overcoming malnutrition throughout the world.

A self-assembling peptide hydrogel for ultrarapid 3D bioassays

Biosensing analytical platforms rely on the intimate structure-function relationship of immobilized probes. In this context, hydrogels are appealing semi-wet systems to locally confine biomolecules while preserving their structural integrity and function. Yet, limitations imposed by biomolecule diffusion rates or fabrication difficulties still hamper their broad application. Here, using a self-assembling peptide, a printable and self-adhesive hydrogel was obtained and applied to fabricate arrays of localized bio-functional 3D microenvironments on analytical interfaces. This soft matrix represents a robust and versatile material, allowing fast and selective tuning of analyte diffusion, which is exploited here to run in-gel immunoassays under solution-like conditions in an unprecedented (<10 min) time frame. The developed material overcomes major limitations associated with hydrogels for bioassays, widening the prospects for easy fabrication of multifunctional bio-interfaces for high-throughput, molecular recognition assays.

Magnet Patterned Superparamagnetic Fe3 O4 /Au Core-Shell Nanoplasmonic Sensing Array for Label-Free High Throughput Cytokine Immunoassay

Rapid and accurate immune monitoring plays a decisive role in effectively treating immune-related diseases especially at point-of-care, where an immediate decision on treatment is needed upon precise determination of the patient immune status. Derived from the emerging clinical demands, there is an urgent need for a cytokine immunoassay that offers unprecedented sensor performance with high sensitivity, throughput, and multiplexing capability, as well as short turnaround time at low system complexity, manufacturability, and scalability. In this paper, a label-free, high throughput cytokine immunoassay based on a magnet patterned Fe3 O4 /Au core-shell nanoparticle (FACSNP) sensing array is developed. By exploiting the unique superparamagnetic and plasmonic properties of the core-shell nanomaterials, a facile microarray patterning technique is established that allows the fabrication of a uniform, self-assembled microarray on a large surface area with remarkable tunability and scalability. The sensing performance of the FACSNP microarray is validated by real-time detection of four cytokines in complex biological samples, showing high sensitivity (≈20 pg mL-1 ), selectivity and throughput with excellent statistical accuracy. The developed immunoassay is successfully applied for rapid determination of the functional immunophenotype of leukemia tumor-associated macrophages, manifesting its potential clinical applications for real-time immune monitoring, early cancer detection, and therapeutic drug stratification toward personalized medicine.